AMBER Archive (2006)

Subject: RE: AMBER: NAD parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 28 2006 - 10:32:48 CDT

Dear Urszula,

> I want to simulate one protein with Zn2+ ion and with NAD. How can I
> prepare NAD.lib? Does anyone have the necessary amber lib for reading
> NAD into leap? Are there any examples I can follow?

There are a number of parameters available here:
http://pharmacy.man.ac.uk/amber/

You can also find a set of NAD+/NADH parameters in
$AMBERHOME/dat/contrib/NADH_and_NAD+

These were based on my doctorate work with LADH. You can find a copy at
http://www.rosswalker.co.uk under reports.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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